Theories common to general fandom

The cast died in the first episode and now they're all in Purgatory. Explicitly Jossed by the creators of Lost, among other writers. There was an infamous (false) rumor that this was how Dungeons & Dragons would end. After being explicitly Jossed, Lostactually ended this way, though its characters ended in Purgatory after they died, either during or after the series, rather than being Dead All Along.

All Just a Dream: This sometimes reflects either some fans' lack of faith in the writers or their lack of imagination; revealing that the whole story was a dream as a Deus ex Machina has been a Dead Horse Trope for quite a while. Variations of this include:

Dying Dream is a very commonly speculated form, especially if the series starts with a near-fatal accident.

The Tommyverse is well-known outside of TV Tropes. Essentially Six Degrees of St. Elsewhere it postulates that every show that has ever crossed-over with St. Elsewhere exists in a shared universe wherein everything takes place entirely within the mind of autistic child Tommy Westphall, and the shows that crossed over with them, and so-on. This ultimately leads to a staggering number of television shows stretching from The X-Files to Arrested Development. On the other end of the spectrum it has sparked some fascinating (and pretentious!) discussions about the nature of intertextuality, metafiction, As Himself, and other such post-modern concepts.

The protagonist is fighting on the wrong side. The agency they work for is secretly working for the enemies, or has a conspiracy going.

The protagonist is fighting on the wrong side, because the "evil" characters are actually in the right and he/she is too blind or prejudiced to notice.

Character X is a mole or traitor who will Face-Heel Turn. Alternatively, villainous Character Y is working for the heroes or will make a Heel-Face Turn. It used to be less common for a villain to receive enough development to make this one plausible unless it was bound to happen; these days, more creators are interested in humanizing the opposition, but that doesn't stop audiences from speculating.

Any fantasy setting is often presumed to be Earth All Along either far in the future or far in the past, the epileptic trees even covering up cases where the dates are explicitly stated through an Unreliable Narrator. For stories that take place in a Constructed World (which isn't supposed to have anything to do with our world): Show X takes place After the End, or else in the distant past and two of the characters are Adam and Eve.

Any "Character X and Character Y are the same person" theories qualify, even when there's no clear reason for one or the other character to change his identity and they don't look anything alike. (Lost gets this a lot, too). By extension, Character X is actually a Shape Shifter or Body Snatcher pretending to be Character X (in universes where they exist).

Any given pair of characters who played a big role in the backstory and then vanished (or one such character and a current character with a mysterious past) will have a theory postulating that they're the same person, usually latching onto minor details in both stories to "prove" it. (Granted, this is more likely than a lot of these theories to be true.)

Show X is set in the same universe as Show Y.

Inversion: The spin-off is not really set in the same universe as the original.

Or sometimes: The spinoff IS set in the same universe as the original

The entire story is an Author Tract regardless of Word of God. Common topics include sexuality, religion, politics, nukes or drugs.

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